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Studies of T cells and their clonally unique receptors have shown promise in elucidating the association between immune response and human disease. Methods to identify T-cell receptor clones which expand or contract in response to certain…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
Non-genetic forms of antimicrobial drug resistance can result from cell-to-cell variability that is not encoded in the genetic material. Data from recent studies also suggest that non-genetic mechanisms can facilitate the development of…
Background: Approximately 40% of adults in Botswana are HIV-infected. The Botswana antiretroviral program began in 2002 and currently treats 34,000 patients with a goal of treating 85,000 patients (~30% of HIV-infected adults) by 2009. We…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
HIV-1 affects tens of millions of people worldwide. Current treatments often involve a cocktail of antiretroviral drugs, which are effective in reducing the virus and extending life spans. However, there is currently no FDA-approved HIV-1…
Hidden Markov models (HMMs) and their variants were successfully used for several sequence annotation tasks. Traditionally, inference with HMMs is done using the Viterbi and posterior decoding algorithms. However, recently a variety of…
Resistance to chemotherapies, particularly to anticancer treatments, is an increasing medical concern. Among the many mechanisms at work in cancers, one of the most important is the selection of tumor cells expressing resistance genes or…
A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene…
Hidden Markov jump processes are an attractive approach for modeling clinical disease progression data because they are explainable and capable of handling both irregularly sampled and noisy data. Most applications in this context consider…
A particular challenge for disease progression modeling is the heterogeneity of a disease and its manifestations in the patients. Existing approaches often assume the presence of a single disease progression characteristics which is…
Dynamic modeling of longitudinal networks has been an increasingly important topic in applied research. While longitudinal network data commonly exhibit dramatic changes in its structures, existing methods have largely focused on modeling…
Cross-sectional HIV incidence estimation leverages recency test results to determine the HIV incidence of a population of interest, where recency test uses biomarker profiles to infer whether an HIV-positive individual was "recently"…
In the context of multilevel longitudinal data, where sample units are collected in clusters, an important aspect that should be accounted for is the unobserved heterogeneity between sample units and between clusters. For this aim we…
The minimum description length (MDL) principle states that the best model to account for some data minimizes the sum of the lengths, in bits, of the descriptions of the model and the residual error. The description length is thus a…
A simple deterministic model is proposed to represent the basic aspects concerning the effects of different antiretroviral treatment schedules on HIV incidence and prevalence of affected populations. The model mimics current treatment…
We aim to model unknown file processing. As the content of log files often evolves over time, we established a dynamic statistical model which learns and adapts processing and parsing rules. First, we limit the amount of unstructured text…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Understanding historical trends in the epidemic of HIV is important for assessing current and projecting future trends in prevalence, incidence and mortality and for evaluating the impact and cost-effectiveness of control measures. In…
Multidrug resistance consists of a series of genetic and epigenetic alternations that involve multifactorial and complex processes, which are a challenge to successful cancer treatments. Accompanied by advances in biotechnology and…